Just two ideas in case the alien AI ever become too efficient, so that all the weapon balance should be retouched:
1/ Degrading moral and AI:
We may consider that, the less the Aliens on any map, the dumber they become (9 of them in a base containment unit (thus perhaps insulated from the outdoor) are like animals).
Thus, inside a Battlescape mission:
- the AI could be degraded the more Aliens are killed.
- the moral management could be made unbalanced in favor to the PHALANX, especially the loss of moral when an Alien is killed, and that would cause the last alien survivors to become insane even more easily as for now (perhaps, currently, they become mad only when they are wounded and they killed one of them).
2/ Toxic UFO wreckage: Currently, there are no Aliens who start the mission already wounded. We might give the alien team some initial handicap on crashed mission by attaching a wreckage model a few perma anti-alien gas fields inside and around it (toxic leaks). Any alien exiting a wreckage would be already partially stunned and demoralized. Of course, it should be tested whether these fields don't prevent too much the Aliens to move and act.